Clover Food Lab chief executive Ayr Muir has never been one to shy away from conflict, using his uncommonly open company blog to air disputes with employees and poke fun at what he considers meaningless “best of” awards given to Clover. And, like many successful people, Muir has a knack for finding the positive in a negative situation.

So when health inspectors tied a recent salmonella outbreak to his chain of vegetarian fast-food restaurants, Muir took the highly unusual step of breaking the news himself, posting updates as the investigation progressed during the nearly two weeks that his operation was shut down. And then he committed himself to becoming a pioneer in food safety.

Muir’s willingness to acknowledge problems and admit mistakes is the product of a sometimes brutal, unfiltered honesty that has made Muir among Boston’s most colorful chief executives. He thinks big, with goals to revolutionize the fast-food industry, grow bigger than McDonald’s, and help save the planet by serving healthy food.

Wendy Maeda/Globe Staff

Customers lined up at the Clover Food Lab in Harvard Square on Friday. It reopened last Thursday.

Still, for all his openness, Muir won’t reveal if he’s a vegetarian. It’s a dirty word, as far as he’s concerned, one he fears could keep committed carnivores from visiting his establishments. He doesn’t even let his workers use the word to describe Clover’s $6 soy BLT sandwiches and $7 egg and eggplant platters, telling them simply to say there is no meat on the menu. The word “healthy” is also banned.

Muir’s passion for meatless fare comes from environmental concerns about global warming. Livestock waste produces methane, a potent greenhouse gas, and getting people to eat less meat could have an impact on slowing climate change, he said. Muir, a distant relative of the naturalist John Muir, is convinced that, like the evolution of gay rights, changes in people’s eating habits could happen quickly.

Clover relies heavily on fresh, locally grown fruits and vegetables, boasting on its website about the fact the restaurants have no freezers. But food safety can be tricky for restaurants that use a lot of fresh produce, which causes nearly half of the most serious food-borne illnesses, according to the Centers for Disease Control and Prevention.

The salmonella outbreak, which sickened at least 27 people, has left Muir determined to adopt new techniques that he hopes could become a model for the restaurant industry. Among the changes he envisions: a technology that can track say, a potato, from farm to truck to kitchen, storing information about everyone who handled it and what temperature it was at every step.

“We can sit back and feel safe if you’re dealing with frozen nuggets going into a fryer,” he said. “It’s pretty hard to screw that up. There’s a lot more places that things can go wrong with fresh food.”

Muir, who has a master’s degree in materials science from MIT and an MBA from Harvard, has a confident air that can rub some people the wrong way. He conducts painstaking research to perfect each item at Clover, and therefore, he said, every employee should like everything on the menu. If they don’t, they need to learn to embrace it so they can believe in what they are selling.

Last February, he discovered his employees were setting the coffee grinder to a finer setting to make coffee for themselves, then switching it back to the more coarse grind mandated for customers.

“It sort of feels like having some of my most trusted managers spit on me,” he wrote on the blog, noting that he and his chef had scoured the country tasting coffee and studying pouring methods to build “the future of coffee.”

But Muir now says this was a mistake, a not-necessarily unusual admission for a man who wrote “We will screw something up” on the wall of his first restaurant in Harvard Square.

Still, for all his openness, Muir won’t reveal if he’s a vegetarian. It’s a dirty word, as far as he’s concerned.

Muir also stirred up controversy when he posted a picture of a 2011 Dig Boston “best food truck/brick and mortar” award in the trash. This followed a post a few weeks earlier about an Improper Bostonian award that also got tossed in the garbage.

“What are these ‘best of’ things anyway?,” he wrote. “They’re a way for these publications to (a) advertise by piggybacking on businesses who are ‘awarded,’ and (b) a way for publishers to drive more traffic to their website/publication.”

A few days later, he wrote that he made “mistake number 8,901 for the year” and had apologized to the owner of Dig Boston over coffee.

Muir blogs constantly about Clover, writing about new sodas he’s developing, new permits he’s applying for, and even a batch of moldy bread that had to be thrown out. And he responds to an overwhelming number of comments.

“He’s very caring and loving and committed to people,” said Muir’s wife, Brooke, a part-time children’s book illustrator who stays home with their three young children in Lincoln. “But he doesn’t spend time worrying about what other people are going to think.”

Muir grew up in Bernardston, in Western Massachusetts, the oldest child of two schoolteachers. He went to Deerfield Academy, then MIT and Harvard, and worked in marketing for Patagonia and as a consultant at McKinsey & Co. Then he started reading about food and the environment and decided he wanted to start a meat-free fast-food company.

To learn about the industry, Muir got part-time jobs at a Burger King in Winchester and Panera Bread in Watertown. He hired an executive chef and in 2008 started testing items in a food truck inspired by one he used to visit at MIT.

Muir’s fledgling empire has expanded quickly, with two restaurants opening in June and two more in the works. Muir is scouting locations in Washington and Philadelphia, and is in talks to put a restaurant inside a Whole Foods store.

From the very beginning, Muir has surveyed customers about what they like and don’t like about his products. The very first item, a chickpea fritter sandwich with falafel and hummus, has gone through 32 versions.

Muir, who does yoga and sometimes rides a motorcycle, constantly seeks customer comments. Employees are taught to solicit feedback from guests and enter their responses into iPods they use to take food orders. Muir reads them all.

“We’re very involved,” said Dylan Sullens, a 20-year-old Berklee College of Music student who works at the Clover food truck in Dewey Square. “I can take something that a customer said, send it the CEO, and then the next day or the next week, the whole company has changed because of it. It’s pretty wild.”

What Muir doesn’t want his employees to do is express their opinions of the food, even if they love it, fearing it will keep customers from giving honest feedback if they disagree.

Clover is a tightly run ship. Order takers are asked to learn the names of at least 200 regular customers in the first six months on the job. The kitchen is expected to get orders out within an average of 3½ minutes. Few deviations from the menu are allowed, not even a request for a slice of lemon in a glass of ice tea.

And, of course, according to the training manual, employees should “NEVER describe Clover as ‘vegetarian.’ ”

Muir has his detractors, including former employees who say he is overly controlling and expects workers to check their individuality at the door. But Muir also wants to do right by his 130 workers. During the shutdown, he took out a $25,000 loan to pay their salaries.

In just a few years, Clover has developed a loyal following, and an hour after the Harvard Square restaurant reopened last Thursday, the spartan space was packed with customers.

Bob Woodbury walked up to Muir to shake his hand, calling himself “an admirer and a regular customer.” Woodbury and his wife, both vegetarians, eat at Clover about once a week.

The Woodburys read Muir’s blog. They know his story. And they like supporting a place that composts waste and uses local produce, but doesn’t make a big deal of not serving meat.

“They don’t make a moral point of the fact that it’s vegetarian,” said Mary Woodbury, a massage therapist. “They don’t put up signs that says, ‘Doing good here.’ They just do good.”

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